Mitogenomic Insights Into the Population Structure and Demographic History of Tree Shrews (Tupaia belangeri) in China

The northern tree shrew (Tupaia belangeri) exhibits significant morphological and geographical variations, but its evolutionary history and subspecies boundaries remain controversial. Here, we analyzed the complete mitochondrial genomes of 63 individuals, representing 12 populations in China to study phylogenetic relationships, genetic diversity, and population history. Phylogenetic analysis consistently restored four mitochondrial branches with strong geographic structures and significant differences. The three lineages correspond to geographically restricted subspecies (T. b. tonquinia, T. b. modesta, and T. b. gaoligongensis), while individuals assigned to several traditional subspecies cluster in a broad mainland lineage (T. b. chinensis, T. b. yunalis, and T. b. yaoshanensis). The divergence time estimate places the origin of the main lineage in the Miocene, consistent with major tectonic and geomorphological events. Demographic analysis revealed different population histories, including varying degrees of expansion in recent continental and island lineages, as well as the long-term stability of T. b. gaoligongensis. Genetic diversity varied markedly among lineages, with the highest diversity observed in the T. b. gaoligongensis and the lowest diversity observed in the T. b. modesta. These findings demonstrate that landscape complexity and demographic history are key drivers of evolutionary diversification in T. belangeri, challenging classical morphology-based subspecies classifications and underscoring the need for comprehensive sampling across both domestic and international ranges.